As has been said there are parts of Luton that are nice, and the town centre is similarly grim to plenty of others. There are issues with gun crime in areas. It's no longer that surprising to me when I hear of it, which is quite sad. I've never felt any more unsafe visiting or working there than in any other city in the region, but then I've never lived there.
I am surprised to see Leighton Buzzard and Milton Keynes suggested as cheap/affordable options. They're not! Unless you opt for one of the rougher areas - MK certainly has areas that are as deprived as Luton.
If you want the transport links and closeness to big towns and cities, then just look at a map and look at the villages either side of the M1 (and/or railway line) as you go north of Luton. Or whichever artery you want to be near.
None of the villages or smaller towns are cheap, but then it's the South East. However, they are cheaper than Luton, MK, and LB. And miles cheaper than Harpenden or St Albans. Although St A does have some nice areas, and the history is worth visiting, I don't enjoy spending time there. I don't much enjoy Harpenden either because it's so busy and crowded and I find it stressful as a result. LB's centre is nicer IMO than Harpenden's and miles easier for parking, etc. I don't feel harassed in LB.
Generally, the towns/villages with a train station will be pricier than the villages circling a station. E.g. Flitwick has a train station (Bedford-Brighton line), Westoning is a village 5 minutes away, and the motorway another 5 or so minutes. And there are multiple other villages of varying sizes, with varying amenities, in between. Some are pretty much hamlets (but may still have a pub), some have a handful of shops, some have a full high street. There's also Ampthill, which I think has been mentioned. Historic centre, and a Waitrose. 
There is a world of different options within reach of Luton, and all with the transport links and closeness to London.
It really depends on what you want. I'm quite happy working, socialising and visiting the big towns/cities, but I would not want to live in them. Whereas I know that's not the case for others.
Several people have described MK as soulless, but I'd disagree. It depends where you base yourself and what you choose to involve yourself in, but a lot of effort goes into creating a sense of community. The way the city was designed means that it's planned as a collection of villages with their own names (hence the above comment about areas of deprivation), all the roads are lined with trees so when you drive around it feels like a really green and leafy area because the houses are hidden, it's filled with parks which are actively managed and offer lots of activities, ...and you can get to Euston station in 35 minutes. But people do keep telling me MK hospital isn't great.
I really like MK and all it has to offer, but I couldn't afford to live there and wouldn't particularly want to (solely because I don't like living in cities). But then there are plenty of separate villages around it if you wanted the best of both. None of the people I know who live in MK would describe it as affordable in terms of house prices, most of them have ended up having to move much further out than they would have liked to be able to afford to live there. And they have decent, well paying jobs. Although I suppose if you're comparing to London or St Albans it is affordable.
I guess if your home is a base and you're happy to travel out to other places to do things then it's different than if you want everything on your doorstep. The newer edges of Dunstable are really nice, have local access to shops and takeaways, and then good transport links to get to bigger/nicer places for other things. Dunstable is more affordable than Luton, LB, MK, and obviously St A and Harpenden, but basically attached to Luton.
I'm not a massive fan of Bedford. Other than the train line it's a pain to get access to motorways, and I hate the town centre with a passion other than if you happen to be right by the river. The outlying Bedford villages are nicer, but I still hate them transport wise. MK is easier than Bedford for travel links.
As for "rough pubs", there was a brawl in one of LB's pubs in the last year which landed a bunch of people in hospital. Pub violence isn't limited to Luton!
Oh, and if you don't already know and end up considering it, the w in Flitwick is silent. 